This script shows how to analyze a typical ISS segmented dataset. The analysis is based on Scanpy (documentation in https://scanpy.readthedocs.io/en/stable/index.html) and Squidpy (documentation in https://squidpy.readthedocs.io/en/stable/)

import packages

create list of sample paths

run segmentation

create anndata

concat anndata objects into one file

filter cells

normalization and transformation

We now save the raw data in adata.raw and apply normalization and log-transformation to minimize the effect of outliers. We also scale the data to give the same importance to all genes in clustering

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